Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia.

Yam Sim Khaw,Faizatul Lela Jafar,Yoke Fun Chan,Norlijah Othman,Hui Yee Chee

doi:10.3389/fmicb.2016.00543

Yam Sim Khaw, Faizatul Lela Jafar + Show 3 more

Open Access

https://doi.org/10.3389/fmicb.2016.00543

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Abstract

Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5′ and 3′ non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63–81% among themselves and 63–96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection.

Highlights

Human rhinovirus (HRV) has been recognized as one of the respiratory viruses associated with common cold in humans since the late 1950s
Due to the higher incidence of Human rhinovirus-C (HRV-C) in causing severe diseases and insufficient availability of HRV-C complete genome sequences for further analyses, the present study aimed to sequence the complete genome of Malaysian HRV-Cs and to perform genetic analyses of these viruses
5′ and 3′ NCR, and the ORF were successfully amplified in this study. These seven Malaysian isolates were isolated from patients displaying a range of respiratory diseases such as bronchiolitis, staphylococcal pneumonia and acute exacerbations of bronchial asthma (AEBA)

Summary

Introduction

Human rhinovirus (HRV) has been recognized as one of the respiratory viruses associated with common cold in humans since the late 1950s. HRV infection is a significant burden that is frequently associated with morbidity and mortality among hospitalized pediatric patients in Malaysia, and worldwide (Etemadi et al, 2013). HRV has more than 100 serotypes, which have been clustered into three groups: HRV-A, B, and C (McIntyre et al, 2013). HRV-A consists of 80 serotypes, HRV-B consists of 32 types, and HRV-C consists of 55 types HRV-C, which was discovered in 2006, is a new species of HRV and has led to the reemergence of research interest in HRV (Lamson et al, 2006; Lau et al, 2007).

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